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Fix Contingency Table #217

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merged 5 commits into from
Nov 8, 2024
Merged

Fix Contingency Table #217

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3b55276
improve main table
FBartos Oct 29, 2024
5adf357
add
FBartos Oct 29, 2024
007500a
fix unit tests
FBartos Oct 29, 2024
4e052ab
add header and change name
FBartos Nov 8, 2024
d308e56
adding the message
FBartos Nov 8, 2024
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1 change: 1 addition & 0 deletions .Rprofile
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
source("renv/activate.R")
96 changes: 53 additions & 43 deletions R/contingencytables.R
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Expand Up @@ -122,6 +122,11 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {

# Output Tables
.crossTabMain <- function(jaspResults, dataset, options, analyses, ready) {

if (!(options$countsObserved || options$countsExpected || options$percentagesRow || options$percentagesColumn ||
options$percentagesTotal || options$residualsUnstandardized || options$residualsPearson || options$residualsStandardized))
return()

for (i in 1:nrow(analyses)){
analysis <- analyses[i,]
analysisContainer <- jaspResults[[.crossTabCreateContainerName(analysis)]]
Expand All @@ -130,12 +135,12 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {

# Create table
crossTabMain <- createJaspTable(title = gettext("Contingency Tables"))
crossTabMain$dependOn(c("countsExpected", "percentagesRow", "percentagesColumn",
crossTabMain$dependOn(c("countsExpected", "countsObserved", "tableMargin", "percentagesRow", "percentagesColumn",
"percentagesTotal", "rowOrder", "columnOrder", "residualsUnstandardized",
"residualsPearson", "residualsStandardized"))
crossTabMain$showSpecifiedColumnsOnly <- TRUE
crossTabMain$position <- 1
#

.crossTabLayersColumns(crossTabMain, analysis)

colTitleHere <- analysis$rows
Expand All @@ -146,35 +151,35 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {

counts.fp <- .crossTabCountsFp(dataset, options)

if (options$countsExpected || options$percentagesRow || options$percentagesColumn ||
options$percentagesTotal || options$residualsUnstandardized || options$residualsPearson ||
options$residualsStandardized)
crossTabMain$addColumnInfo(name = "type[counts]", title = "", type = "string")
if (options$countsExpected) crossTabMain$addColumnInfo(name = "type[expected]", title = "", type = "string")
if (options$percentagesRow) crossTabMain$addColumnInfo(name = "type[row.proportions]", title = "", type = "string")
if (options$percentagesColumn) crossTabMain$addColumnInfo(name = "type[col.proportions]", title = "", type = "string")
if (options$percentagesTotal) crossTabMain$addColumnInfo(name = "type[total.proportions]", title = "", type = "string")
if (options$residualsUnstandardized) crossTabMain$addColumnInfo(name = "type[unstandardized.residuals]",title = "", type = "string")
if (options$residualsPearson) crossTabMain$addColumnInfo(name = "type[pearson.residuals]", title = "", type = "string")
if (options$residualsStandardized) crossTabMain$addColumnInfo(name = "type[standardized.residuals]", title = "", type = "string")
if (sum(options$countsObserved, options$countsExpected, options$percentagesRow, options$percentagesColumn,
options$percentagesTotal, options$residualsUnstandardized, options$residualsPearson, options$residualsStandardized) > 1) {
if (options$countsObserved) crossTabMain$addColumnInfo(name = "type[counts]", title = "", type = "string")
if (options$countsExpected) crossTabMain$addColumnInfo(name = "type[expected]", title = "", type = "string")
if (options$percentagesRow) crossTabMain$addColumnInfo(name = "type[row.proportions]", title = "", type = "string")
if (options$percentagesColumn) crossTabMain$addColumnInfo(name = "type[col.proportions]", title = "", type = "string")
if (options$percentagesTotal) crossTabMain$addColumnInfo(name = "type[total.proportions]", title = "", type = "string")
if (options$residualsUnstandardized) crossTabMain$addColumnInfo(name = "type[unstandardized.residuals]",title = "", type = "string")
if (options$residualsPearson) crossTabMain$addColumnInfo(name = "type[pearson.residuals]", title = "", type = "string")
if (options$residualsStandardized) crossTabMain$addColumnInfo(name = "type[standardized.residuals]", title = "", type = "string")
}

.crossTabMainOvertitle(dataset, options, crossTabMain, analysis, counts.fp)

# Totals columns
totalTitle <- gettext("Total")
if (counts.fp || options$countsExpected || options$percentagesRow || options$percentagesColumn ||
options$percentagesTotal || options$residualsUnstandardized || options$residualsPearson ||
options$residualsStandardized) {
crossTabMain$addColumnInfo(name = "total[counts]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$countsExpected) crossTabMain$addColumnInfo(name = "total[expected]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$percentagesRow) crossTabMain$addColumnInfo(name = "total[row.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$percentagesColumn) crossTabMain$addColumnInfo(name = "total[col.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$percentagesTotal) crossTabMain$addColumnInfo(name = "total[total.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$residualsUnstandardized) crossTabMain$addColumnInfo(name = "total[unstandardized.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsPearson) crossTabMain$addColumnInfo(name = "total[pearson.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsStandardized) crossTabMain$addColumnInfo(name = "total[standardized.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
} else
crossTabMain$addColumnInfo(name = "total[counts]", title = totalTitle, type = "integer")

if (options$tableMargin && (counts.fp || options$countsExpected || options$percentagesRow || options$percentagesColumn ||
options$percentagesTotal || options$residualsUnstandardized || options$residualsPearson || options$residualsStandardized)) {
if (options$countsObserved) crossTabMain$addColumnInfo(name = "total[counts]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$countsExpected) crossTabMain$addColumnInfo(name = "total[expected]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$percentagesRow) crossTabMain$addColumnInfo(name = "total[row.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$percentagesColumn) crossTabMain$addColumnInfo(name = "total[col.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$percentagesTotal) crossTabMain$addColumnInfo(name = "total[total.proportions]", title = totalTitle, type = "number", format = "dp:1;pc")
if (options$residualsUnstandardized) crossTabMain$addColumnInfo(name = "total[unstandardized.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsPearson) crossTabMain$addColumnInfo(name = "total[pearson.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsStandardized) crossTabMain$addColumnInfo(name = "total[standardized.residuals]", title = totalTitle, type = "number", format = "sf:4;dp:2")
} else if (options$tableMargin)
if (options$countsObserved) crossTabMain$addColumnInfo(name = "total[counts]", title = totalTitle, type = "integer")

analysisContainer[["crossTabMain"]] <- crossTabMain
analysis <- as.list(analysis)
Expand Down Expand Up @@ -413,14 +418,14 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {
pr.type <- "number"
}

table$addColumnInfo(name = paste0(column.name,"[counts]"), title = myTitle, type = pr.type, format = pr.format, overtitle = overTitle)
if (options$countsExpected) table$addColumnInfo(name = paste0(column.name,"[expected]"), title = myTitle, type = "number", format = "sf:4;dp:2")
if (options$percentagesRow) table$addColumnInfo(name = paste0(column.name,"[row.proportions]"), title = myTitle, type = "number", format = "dp:1;pc")
if (options$percentagesColumn) table$addColumnInfo(name = paste0(column.name,"[col.proportions]"), title = myTitle, type = "number", format = "dp:1;pc")
if (options$percentagesTotal) table$addColumnInfo(name = paste0(column.name,"[total.proportions]"), title = myTitle, type = "number", format = "dp:1;pc")
if (options$residualsUnstandardized) table$addColumnInfo(name = paste0(column.name,"[unstandardized.residuals]"),title = myTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsPearson) table$addColumnInfo(name = paste0(column.name,"[pearson.residuals]"), title = myTitle, type = "number", format = "sf:4;dp:2")
if (options$residualsStandardized) table$addColumnInfo(name = paste0(column.name,"[standardized.residuals]"), title = myTitle, type = "number", format = "sf:4;dp:2")
if (options$countsObserved) table$addColumnInfo(name = paste0(column.name,"[counts]"), title = myTitle, type = pr.type, format = pr.format, overtitle = overTitle)
if (options$countsExpected) table$addColumnInfo(name = paste0(column.name,"[expected]"), title = myTitle, type = "number", format = "sf:4;dp:2", overtitle = overTitle)
if (options$percentagesRow) table$addColumnInfo(name = paste0(column.name,"[row.proportions]"), title = myTitle, type = "number", format = "dp:1;pc", overtitle = overTitle)
if (options$percentagesColumn) table$addColumnInfo(name = paste0(column.name,"[col.proportions]"), title = myTitle, type = "number", format = "dp:1;pc", overtitle = overTitle)
if (options$percentagesTotal) table$addColumnInfo(name = paste0(column.name,"[total.proportions]"), title = myTitle, type = "number", format = "dp:1;pc", overtitle = overTitle)
if (options$residualsUnstandardized) table$addColumnInfo(name = paste0(column.name,"[unstandardized.residuals]"),title = myTitle, type = "number", format = "sf:4;dp:2", overtitle = overTitle)
if (options$residualsPearson) table$addColumnInfo(name = paste0(column.name,"[pearson.residuals]"), title = myTitle, type = "number", format = "sf:4;dp:2", overtitle = overTitle)
if (options$residualsStandardized) table$addColumnInfo(name = paste0(column.name,"[standardized.residuals]"), title = myTitle, type = "number", format = "sf:4;dp:2", overtitle = overTitle)
}
}

Expand Down Expand Up @@ -882,7 +887,8 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {
row[["total[counts]"]] <- sum
else row[["total[counts]"]] <- as.integer(sum)

row <- c(row.count, row)
if (options$countsObserved)
row <- c(row.count, row)

if (options$countsExpected)
row <- c(row, .crossTabCountsMatrixToRow(expected.matrix,
Expand Down Expand Up @@ -924,7 +930,7 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {
row[[var.name]] <- dimnames(counts.matrix)[[1]][j]
row <- .crossTabLayerNames(row, group)

if (j == 1 && !options$countsExpected && !options$percentagesRow &&
if (j == 1 && !options$countsObserved && !options$countsExpected && !options$percentagesRow &&
!options$percentagesCol && !options$percentagesTotal &&
!options$residualsUnstandardized && !options$residualsPearson && !options$residualsStandardized)
row[[".isNewGroup"]] <- TRUE
Expand All @@ -937,13 +943,15 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {
names(row) <- paste0(names(row),"[counts]")
sum <- sum(counts.matrix)

if(counts.fp || options$countsExpected || options$percentagesRow ||
if(options$tableMargin && (counts.fp || options$countsExpected || options$percentagesRow ||
options$percentagesColumn || options$percentagesTotal || options$residualsUnstandardized ||
options$residualsPearson || options$residualsStandardized)
options$residualsPearson || options$residualsStandardized))
row[["total[counts]"]] <- sum
else row[["total[counts]"]] <- as.integer(sum)
else if (options$tableMargin)
row[["total[counts]"]] <- as.integer(sum)

row <- c(row.count, row)
if (options$countsObserved)
row <- c(row.count, row)

if (options$countsExpected) {
expected <- .crossTabCountsColumnTotalsMatrixToRow(expected.matrix, counts.matrix, type = "expected")
Expand Down Expand Up @@ -973,13 +981,15 @@ ContingencyTablesInternal <- function(jaspResults, dataset, options, ...) {
if(var.name != "")
row[[var.name]] <- gettext("Total")

if (!(options$countsExpected || options$percentagesRow || options$percentagesCol ||
if (!(options$countsObserved || options$countsExpected || options$percentagesRow || options$percentagesCol ||
options$percentagesTotal || options$residualsUnstandardized || options$residualsPearson ||
options$residualsStandardized))
row[[".isNewGroup"]] <- TRUE

row <- .crossTabLayerNames(row, group)
rows[[length(rows) + 1]] <- row
if (options$tableMargin) {
row <- .crossTabLayerNames(row, group)
rows[[length(rows) + 1]] <- row
}
counts.rows <- c(counts.rows, rows)
}

Expand Down
4 changes: 4 additions & 0 deletions inst/qml/ContingencyTables.qml
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Expand Up @@ -114,6 +114,7 @@ Form
Group
{
title: qsTr("Counts")
CheckBox { name: "countsObserved"; label: qsTr("Observed"); checked: true }
CheckBox { name: "countsExpected"; label: qsTr("Expected") }
CheckBox
{
Expand Down Expand Up @@ -148,6 +149,9 @@ Form
CheckBox { name: "percentagesColumn"; label: qsTr("Column") }
CheckBox { name: "percentagesTotal"; label: qsTr("Total") }
}


CheckBox { name: "tableMargin"; label: qsTr("Table margin"); checked: true }
}

Section
Expand Down
4 changes: 3 additions & 1 deletion inst/qml/ContingencyTablesBayesian.qml
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Expand Up @@ -107,7 +107,7 @@ Form
Group
{
title: qsTr("Counts")
debug: true
CheckBox { name: "countsObserved"; label: qsTr("Observed"); checked: true }
CheckBox { name: "countsExpected"; label: qsTr("Expected") }
}

Expand All @@ -127,6 +127,8 @@ Form
CheckBox { name: "percentagesColumn"; label: qsTr("Column") }
CheckBox { name: "percentagesTotal"; label: qsTr("Total") }
}

CheckBox { name: "tableMargin"; label: qsTr("Table margin"); checked: true }
}

Section
Expand Down
7 changes: 7 additions & 0 deletions renv/.gitignore
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@@ -0,0 +1,7 @@
library/
local/
cellar/
lock/
python/
sandbox/
staging/
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